The environment experienced throughout ontogeny plays an important role in shaping the patterns of phenotypic variation within and among individuals. Particularly, stressful factors are thought to affect the mechanisms that buffer the development, resulting in an increase of phenotypic variance. In this study we examine the effect of an environmental stressor, protein-caloric restriction, on levels of disparity and fluctuating asymmetry of the skull shape. The experimental design consisted in the application of different levels of nutrient restriction during postnatal life to four groups of Wistar rats. Sixty two 3D landmarks from both sides of the skull were digitized on micro CT-scans obtained from animals aged 63 days. A two-way mixed model ANOVA was applied to the coordinates after Procrustes superimposition in order to simultaneously estimate the amount of fluctuating (FA) and directional asymmetry. FA scores for each individual were calculated and used for testing the differences in FA between treatments. The sum of the Euclidean distances between individuals along the principal component axis was used as a measure of within group disparity. We found that the early nutrient restriction led to a significant increase of shape disparity. In addition, FA was significant higher than measurement error and accounted for between 10 to 17% of the total shape variation within-groups in the face, base and vault. However, no effect of stress on levels of FA was found in either module of the skull. The implications of these results are discussed in the context of human population studies.